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Introduction

Zombi is a flexible platform of genome evolution written in Python 3.6 that can be used to generate species trees, genomes and sequences.

The three main basic modes

There are three main modes to run Zombi: T (species Tree), G (Genomes) and S (Sequences)

You must run the computations in sequential order. This means that: Computing genomes requires having computed previously a species tree computed with the T mode and computing sequences requires having computed previously genomes with the G mode.

• Generating Species Trees (T)

• Generating Genomes (G)

• Generating a Sequences (S)

Besides these three main modes, there are other 7 advanced modes that you can use to obtain species tree, genomes and sequences using different evolutionary models. Here you can see a table summarizing all the currently existing modes in Zombi: